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378d
From Proteopedia
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|PDB= 378d |SIZE=350|CAPTION= <scene name='initialview01'>378d</scene>, resolution 2.400Å | |PDB= 378d |SIZE=350|CAPTION= <scene name='initialview01'>378d</scene>, resolution 2.400Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=378d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=378d OCA], [http://www.ebi.ac.uk/pdbsum/378d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=378d RCSB]</span> | ||
}} | }} | ||
| Line 24: | Line 27: | ||
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
[[Category: Wahl, M C.]] | [[Category: Wahl, M C.]] | ||
| - | [[Category: DMY]] | ||
| - | [[Category: NA]] | ||
[[Category: double drug in minor groove]] | [[Category: double drug in minor groove]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: right handed dna]] | [[Category: right handed dna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:56 2008'' |
Revision as of 02:21, 31 March 2008
| |||||||
| , resolution 2.400Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF THE SIDE-BY-SIDE BINDING OF DISTAMYCIN TO DNA
Overview
The 2.40 A resolution crystal structure of a side-by-side binding of distamycin A molecules to a DNA octamer d(GTATATAC)2 with an extended alternating TA sequence has been determined. The unit-cell parameters are a = 29.55, b = 42.18, c = 43.38 A, beta = 96.56 degrees, space group P21, with two molecules in the asymmetric unit, in contrast to all previous side-by-side distamycin-DNA complexes which have only a single DNA strand and one drug molecule in the asymmetric unit. The structure was solved by the molecular-replacement method and refined to an R index of 21.0% using 3467 reflections [>/= 2sigma(F)]. The minor grooves of the DNA molecules bind two side-by-side antiparallel staggered distamycins spanning about five base pairs and virtually covering the entire length of the DNA. The octamer duplexes exhibit low-high alternations in the helical twist, sugar puckering and the C-O3' and O3'-P torsion angles, similar to the earlier side-by-side complexes containing inosine bases. The molecules are stacked one over the other along the ac diagonal in an infinite pseudo-continuous helical column with no lateral interactions.
About this Structure
378D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of the side-by-side binding of distamycin to d(GTATATAC)2., Mitra SN, Wahl MC, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 1999 Mar;55(Pt 3):602-9. PMID:10089456
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